Manganese in PDB 5hrk: The Crystal Structure of Asfvpolx(H115F Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex

The structure of The Crystal Structure of Asfvpolx(H115F Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex, PDB code: 5hrk was solved by Y.Q.Chen, J.Zhang, J.H.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.03 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	106.726, 87.196, 82.616, 90.00, 97.59, 90.00
R / Rfree (%)	23.3 / 27.3

The binding sites of Manganese atom in the The Crystal Structure of Asfvpolx(H115F Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex (pdb code 5hrk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Crystal Structure of Asfvpolx(H115F Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex, PDB code: 5hrk:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the The Crystal Structure of Asfvpolx(H115F Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Asfvpolx(H115F Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:69.5 occ:1.00 OD2 A:ASP51 1.8 90.6 1.0 OD1 A:ASP49 2.0 87.0 1.0 O3G A:DGT201 2.2 84.4 1.0 O2A A:DGT201 2.4 81.8 1.0 O2B A:DGT201 2.4 68.0 1.0 CG A:ASP51 2.8 80.5 1.0 O A:HOH301 2.9 62.7 1.0 O3A A:DGT201 2.9 80.1 1.0 PB A:DGT201 3.0 64.9 1.0 O A:ASP49 3.1 72.9 1.0 PA A:DGT201 3.2 74.1 1.0 CG A:ASP49 3.2 75.2 1.0 OD1 A:ASP51 3.2 67.2 1.0 PG A:DGT201 3.3 71.4 1.0 O3B A:DGT201 3.3 51.5 1.0 MN A:MN203 3.6 74.7 1.0 C A:ASP49 3.9 79.9 1.0 OD2 A:ASP49 3.9 55.1 1.0 O5' A:DGT201 4.0 56.4 1.0 CB A:ASP51 4.1 72.9 1.0 OG A:SER39 4.1 70.6 1.0 O2G A:DGT201 4.2 67.4 1.0 N A:ASP49 4.3 91.0 1.0 C5' A:DGT201 4.4 71.2 1.0 O1G A:DGT201 4.4 55.0 1.0 CB A:ASP49 4.4 80.0 1.0 N A:SER39 4.4 79.6 1.0 CA A:ASP49 4.4 80.0 1.0 O1B A:DGT201 4.5 47.4 1.0 O1A A:DGT201 4.5 59.4 1.0 CB A:SER39 4.6 76.9 1.0 N A:ASP51 4.7 64.5 1.0 N A:VAL50 4.8 71.1 1.0 CA A:GLY38 4.9 73.3 1.0 C A:VAL50 5.0 67.9 1.0

Manganese binding site 2 out of 4 in the The Crystal Structure of Asfvpolx(H115F Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Asfvpolx(H115F Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:74.7 occ:1.00 O2A A:DGT201 1.8 81.8 1.0 OD2 A:ASP100 2.0 98.4 1.0 OD1 A:ASP51 2.1 67.2 1.0 OD2 A:ASP49 2.5 55.1 1.0 CG A:ASP51 2.9 80.5 1.0 PA A:DGT201 2.9 74.1 1.0 CG A:ASP100 3.2 77.9 1.0 OD2 A:ASP51 3.2 90.6 1.0 OD1 A:ASP49 3.2 87.0 1.0 O1A A:DGT201 3.2 59.4 1.0 CG A:ASP49 3.3 75.2 1.0 C5' A:DGT201 3.6 71.2 1.0 MN A:MN202 3.6 69.5 1.0 O5' A:DGT201 3.7 56.4 1.0 CB A:ASP100 3.9 66.1 1.0 CB A:ASP51 4.1 72.9 1.0 OD1 A:ASP100 4.2 72.6 1.0 O3A A:DGT201 4.2 80.1 1.0 C3' F:DA9 4.5 76.9 1.0 OP1 F:DA9 4.6 78.4 1.0 CZ A:PHE102 4.7 72.2 1.0 O3G A:DGT201 4.7 84.4 1.0 CB A:ASP49 4.7 80.0 1.0 NE2 A:GLN98 4.8 71.4 1.0 O2B A:DGT201 4.9 68.0 1.0 CE2 A:PHE102 4.9 67.2 1.0

Manganese binding site 3 out of 4 in the The Crystal Structure of Asfvpolx(H115F Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of Asfvpolx(H115F Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn202 b:73.0 occ:1.00 O2A B:DGT201 1.8 67.5 1.0 O3G B:DGT201 2.0 76.6 1.0 OD2 B:ASP51 2.0 77.6 1.0 O2B B:DGT201 2.4 93.2 1.0 OD1 B:ASP49 2.7 0.5 1.0 O B:HOH301 2.7 55.4 1.0 OD2 B:ASP49 2.9 58.0 1.0 PA B:DGT201 2.9 68.2 1.0 CG B:ASP49 3.1 84.4 1.0 O3A B:DGT201 3.1 76.8 1.0 CG B:ASP51 3.1 71.7 1.0 PB B:DGT201 3.2 79.8 1.0 PG B:DGT201 3.2 81.6 1.0 OG B:SER39 3.2 91.1 1.0 O B:ASP49 3.4 83.4 1.0 O3B B:DGT201 3.6 79.9 1.0 MN B:MN203 3.6 63.6 1.0 OD1 B:ASP51 3.6 58.8 1.0 O5' B:DGT201 3.8 71.2 1.0 O1G B:DGT201 4.1 50.7 1.0 C B:ASP49 4.1 75.6 1.0 C5' B:DGT201 4.2 75.7 1.0 O1A B:DGT201 4.2 65.6 1.0 O2G B:DGT201 4.3 0.6 1.0 N B:SER39 4.3 73.5 1.0 CB B:ASP51 4.3 61.8 1.0 CB B:ASP49 4.4 83.4 1.0 CB B:SER39 4.5 74.0 1.0 O1B B:DGT201 4.6 81.6 1.0 N B:ASP49 4.6 65.2 1.0 CA B:ASP49 4.6 72.4 1.0 CA B:GLY38 4.7 63.9 1.0 N B:ASP51 4.8 64.1 1.0 N B:VAL50 5.0 69.5 1.0 C B:GLY38 5.0 75.2 1.0

Manganese binding site 4 out of 4 in the The Crystal Structure of Asfvpolx(H115F Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of Asfvpolx(H115F Mutant): 1NT-Gap(P) DNA2:Dgtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn203 b:63.6 occ:1.00 OD2 B:ASP100 1.8 0.4 1.0 O2A B:DGT201 2.3 67.5 1.0 OD1 B:ASP51 2.6 58.8 1.0 OD2 B:ASP49 2.7 58.0 1.0 CG B:ASP49 3.0 84.4 1.0 OD1 B:ASP49 3.0 0.5 1.0 CG B:ASP100 3.0 94.8 1.0 O1A B:DGT201 3.1 65.6 1.0 PA B:DGT201 3.2 68.2 1.0 CG B:ASP51 3.4 71.7 1.0 OD2 B:ASP51 3.5 77.6 1.0 MN B:MN202 3.6 73.0 1.0 OP1 C:DA9 3.6 90.6 1.0 OD1 B:ASP100 3.9 76.2 1.0 CB B:ASP100 4.0 81.5 1.0 C5' B:DGT201 4.1 75.7 1.0 O5' B:DGT201 4.2 71.2 1.0 NE2 B:GLN98 4.2 74.8 1.0 CB B:ASP49 4.3 83.4 1.0 C3' C:DA9 4.4 0.2 1.0 O3A B:DGT201 4.6 76.8 1.0 C4' C:DA9 4.7 0.1 1.0 O3G B:DGT201 4.7 76.6 1.0 CB B:ASP51 4.9 61.8 1.0 C5' C:DA9 5.0 0.6 1.0 P C:DA9 5.0 0.7 1.0

Y.Q.Chen, J.Zhang, J.H.Gan. The Crystal Structure of Se-Asfvpolx(L52/163M Mutant) in Complex with 1NT-Gap DNA1 To Be Published.